amino acid structure and function Flashcards
what isomers are usually dealt with in biology
L isomers
hydrophobic amino acids
glycine alanine proline valine leucine isoleucine methionine tryptophan phenylalanine
polar amino acids
serine threonine tyrosine asparagine glutamine cysteine
which amino acids can participate in redox rxns?
cysteine
disulfide linkages
charged (+) amino acids
basic
lysine
arginine
histidine
charged (-) amino acids
acidic
aspartate (aspartic acid)
glutamate (glutamic acid)
small amino acids
alanine
glycine
cysteine
serine
proline
threonine
aspartic acid
asparagine
medium amino acids
valine
histidine
glutamic acid
glutamine
large amino acids
isoleucine leucine methionine lysine arginine
tyrosine
tryptophan
phenylalanine
essential amino acids
humans cannot synthesize; cannot make or cannot make enough
histidine lysine tryptophan isoleucine phenylalanine valine leucine threonine
consumption > production:
arginine
methionine
nonessential amino acids
humans can synthesize dev novo
alanine cysteine glycine asparagine glutamine proline aspartic acid glutamic acid serine
secondary synthesis:
tyrosine (can make it, but make it from a nonessential amino acid-phenylalanine
mnemonic for essential amino acids
Pvt Tim Hall (first letter of full name)
P henylalanine (Phe, F) V aline (Val, V) T ryptophan (Trp, W)
T hreonine (Thr, T) I soleucine (Ile, I) M ethionine (Met, M)
H istidine (His, H) A rginine (Arg, R) L ysine (Lys, K) L eucine (Leu, L)
proteinogenic amino acids
are used to make proteins from the genetic code
nonproteinogenic amino acids
are not decoded from the genome
e.x. post-translational modifications (phosphorylation for example)
21st amino acid
Selenocysteine (Sec, U)
pKa = 5.2
synthesized from serine
selenocysteine can be processed to:
selenomethionine in plants, algae, and yeast
and alanine in animals
stop codon for selenocysteine
UGA (opal)
selenocysteine is found in
all 3 domains of life (bacteria, archea, and eukaryea)
selenocysteine uses its own
tRNA and SECIS (selenocysteine insertion sequence)
proteins that incorporate Sec are called
selenoproteins
selenoproteins are important for good health:
reduce oxidative stresses in conjunction with vitamin E
required in cerebellum neurons (growth and coordination)
moderate inflammatory responses (may reduce IBD)
what happens to a selenoprotein when Sec is not available
usually a stop codon –> proteins ends up truncated
selenium deficiency results in
2.
- myopathies
keshan disease (cardiomyopathy
- caused by not enough selenium in the diet
- oxidative stress is disinhibited
- treated with Se supplements
statin intolerance (rhabdomyolysis-muscle death)
- statins inhibit Sec-tRNA
- treated by discontinuing statin
- Immune-incompetence
statins are drugs that
block the formation of cholesterol in the liver
too much selenocysteine results in
hair and nail brittleness, “garlic breath”
gastrointestinal/neurological leions
myopathies, renal failure, and death
22nd amino acid
pyrrolysine (Pyl, O)
made by combining 2 lysines
stop codon for pyrrolysine
UAG (amber)
pyrrolysine is found
in some prokaryotes, all are methanogens
pyrrolysine uses its own
tRNA
several members of the human intestinal microbiome make/use Pyl) including
methanomassiliicoccus luminyensis (arahaea)
bilophila wadsorthia (eubacteria)
nonproteinogenic amino acids include
post-translation additions to proteinogenic amino acids
D-enantiomers
metabolism intermediates
pre-biotic or extraterrestrial origin
proteins made by non-riboosomal protein synthesis
A/Adenylation
activation carboxyl
PCP/Peptidyl carrier
elongation intermediate
C/Condensation
peptide bond formation
TE/Thioesterase
release of cyclization
most antibiotics are made by
non-ribosomal protein synthesis
newest class of antibiotics
odilorhabdins
statins are made by
polyketide synthesis (PKS)
primary structure
chain of amino acids
secondary structure
local folding of the polypeptide chain, connected by hydrogen bonds
alpha helices and beta sheet
tertiary structure
folding of the secondary structure, connected by disulfide linkages
quaternary structure
interaction of multiple peptides
polypeptide chains start from _____ and go towards _____
amino side
carboxyl side
peptide bond
bond between carbon and nitrogen
because amino acids are joined by a single bond,
rotation is possible
